c-zhou/yahs: YaHS-1.2a

In this release, the mapping quality score is added to the binary file, which makes the BIN files generated with the previous versions not compatible anymore. If you see error messages indicating the BIN file is not valid, you need to run YaHS with a BED or BAM file to regenerate a BIN file.

This change mainly aims to reduce false-positive contig breaks in repetitive regions. When mapping quality filtering is applied, the HiC coverage in these regions is usually low, leading to excessive contig breaks. It is therefore highly recommended to keep low mapping quality reads in the YaHS input file. All the reads will be used in the contig error detection stage. In the scaffolding stage, the parameter -q (10 by default) is applied to select valid read pairs.